Snakemake pipeline for simulating shotgun metagenomic samples

Quantitative metagenomic alignment and taxonomic exact-matching

This repository contains scripts to run 9 different shotgun metagenomics profiling software on a rat tissue dataset as well as scripts for their downstream analysis (import into R, alpha/beta diversity, & differential abundant analysis).

A Nextflow shotgun metagenomics pipeline with Illumina reads. / Pipeline Nextflow de métagénomique de type shotgun avec des séquences Illumina.

Material para o curso Análise de dados de Metagenômica, organizado pelo Prof. Rodrigo Dalmolin, do Centro Multiusuário de Bioinformática da UFRN

Data Carpentry workshop organised at Utrecht University Medical Center on December 8-9, 2022.

This repository contains the code for ShotgunMG, a Nextflow bioinformatic pipeline for high-resolution metagenomics

🦇🧫📊Study on bat gut shotgun metagenomics

Here we discuss strategies and workflows to analyse metagenomics datasets

Microbiome and bioinformatics workflows for 16S rRNA, shotgun metagenomics, and network analysis.

Comparing 3 different metagenomics approaches with ONT's long read sequencing method

Reproducible research notes, starter commands, and public resources for microbiome, shotgun metagenomics, transcriptomics, and proteomics workflows.

A downstream companion for MetaPhlAn (nf-core/taxprofiler), enabling HUMAnN functional and RGI/CARD AMR profiling from shotgun metagenomes.

Multi-omics characterization of the oral-gut-brain axis in Parkinson's disease using shotgun metagenomics, microbial biomarker discovery, and machine learning.